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Changes in Saccharomyces cerevisiae mRNA abundance following oxidative stress and DNA damage stress

ABSTRACT: We subjected yeast to two stresses, oxidative stress, which under current settings induces a fast and transient response in mRNA abundance, and DNA damage, which triggers a slow enduring response. Using microarrays we performed a conventional quantification of change in mRNA abundance. Keywords: Two separate time courses Overall design: We used Affymetrix microarrays to quantify changes in mRNA abundance following oxidative stress (using hydrogen peroxide) and DNA damage stress (using methyl methanesulfonate) during a three-hour time course (0, 30 min, 60 min, 100 min, 140 min, 180 min).

INSTRUMENT(S): [Yeast_2] Affymetrix Yeast Genome 2.0 Array

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Ophir Shalem

PROVIDER: GSE12220 | GEO | 2008-10-01

SECONDARY ACCESSION(S): PRJNA113853

REPOSITORIES: GEO

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Project description:Background: As carbon sources are exhausted, Saccharomyces cerevisiae cells exhibit reduced metabolic activity and cultures enter stationary phase. We asked whether cells in stationary-phase cultures respond to additional stress at the level of transcript abundance. Results: Microarrays were used to quantify changes in transcript abundance in cells from stationary-phase cultures. In response to oxidative stress, more than 800 mRNAs increased within 1 minute. A significant number of these mRNAs encode proteins involved in stress responses. We tested whether mRNA increases were due to new transcription, rapid poly-adenylation of message (which would not be detected by microarrays), or potential release of mature mRNA sequestered in the cell but insoluble during RNA isolation. Examination of the response to oxidative stress in an RNA polymerase II mutant, rpb1-1 suggested new transcription was not required. Quantitative RT-PCR analysis of a subset of these transcripts further suggested that essentially all isolated transcripts were polyadenylated. In contrast, over 1000 transcripts increased after protease treatment of cell-free lysates from stationary-phase but not exponentially growing cultures. We also determined that oxidative stress and temperature upshift led to the release of different transcripts, suggesting that mRNA release is stress specific. Conclusions: A large number of mRNAs are sequestered in a protease-labile, rapidly releasable form in cells in stationary-phase cultures but not exponentially growing cultures. The differences between mRNAs released by protease treatment and those observed with oxidative stress and temperature upshift, suggest different stresses cause the release of different transcripts. We hypothesize that P-bodies are involved in this sequestration. Keywords: stress response Overall design: This reference Series links data in the following related Series: GSE2263 10s oxidative stress GSE3683 Oxidative Stress 30-min interval GSE3684 Hot phenol GSE3685 RNA polymerase II GSE3686 Protease Treatment GSE3687 Temperature Upshift GSE3688 Oxidative Stress 1-min interval

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Changes in Saccharomyces cerevisiae mRNA abundance following oxidative stress and DNA damage stress

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